Molecular Characterization of Jatropha curcas Resources and Identification of Population-Specific Markers

Jatropha curcas L. is cited as one of the best candidates for future oil and biodiesel production. It is widespread in many tropical and subtropical countries but has not yet received much genetic improvement. The objective of this study was to collect Jatropha germplasm and characterize it with molecular markers. A total of 64 genotypes, collected from seven geographic locations on two continents, were analyzed with 32 simple sequence repeat and two candidate gene-specific primers (ISPJ-1 gene and Curcin-P2 gene promoter). In general, markers were found to be highly conserved, and many (40%) were monomorphic in the studied populations. Polymorphic primers, which amplified population-specific fragments, were identified. The polymorphic information content of the polymorphic markers ranged from 0.03 to 0.47. Genetic similarity analysis identified two distinct groups at 0.73 DICE similarity coefficient. Group I included germplasm collected from the islands of Cuba and Cape Verde, and group II consisted of Brazil, Mozambique, and Senegal populations. Island genotypes were found to be very distinct compared to their mainland counterparts. Sequencing of monomorphic fragments identified single nucleotide polymorphism (SNP) between these two groups. High-resolution melting analysis of the SNP in the Jcps9 locus further confirmed the two gene pools. Sequencing of polymorphic fragments of the Jc03 locus identified a deletion in a (GT)4 repeat motif in the genotypes in group II. Several population-specific microsatellites and SNP markers have been recognized. The distinct Jatropha genotypes and the population-specific molecular markers identified in this study will be valuable resources in breeding programs

Molecular discrimination of tall fescue morphotypes in association with <i>Festuca</i> relatives

<div><p>Tall fescue (<i>Festuca arundinacea</i> Schreb.) is an important cool-season perennial grass species used as forage and turf, and in conservation plantings. There are three morphotypes in hexaploid tall fescue: Continental, Mediterranean and Rhizomatous. This study was conducted to develop morphotype-specific molecular markers to distinguish Continental and Mediterranean tall fescues, and establish their relationships with other species of the <i>Festuca</i> genus for genomic inference. Chloroplast sequence variation and simple sequence repeat (SSR) polymorphism were explored in 12 genotypes of three tall fescue morphotypes and four <i>Festuca</i> species. Hypervariable chloroplast regions were retrieved by using 33 specifically designed primers followed by sequencing the PCR products. SSR polymorphism was studied using 144 tall fescue SSR primers. Four chloroplast (NFTCHL17, NFTCHL43, NFTCHL45 and NFTCHL48) and three SSR (nffa090, nffa204 and nffa338) markers were identified which can distinctly differentiate Continental and Mediterranean morphotypes. A primer pair, NFTCHL45, amplified a 47 bp deletion between the two morphotypes is being routinely used in the Noble Research Institute’s core facility for morphotype discrimination. Both chloroplast sequence variation and SSR diversity showed a close association between Rhizomatous and Continental morphotypes, while the Mediterranean morphotype was in a distant clade. <i>F</i>. <i>pratensis</i> and <i>F</i>. <i>arundinacea</i> var. <i>glaucescens</i>, the P and G1G2 genome donors, respectively, were grouped with the Continental clade, and <i>F</i>. <i>mairei</i> (M1M2 genome) grouped with the Mediterranean clade in chloroplast sequence variation, while both <i>F</i>. <i>pratensis</i> and <i>F</i>. <i>mairei</i> formed independent clade in SSR analysis. Age estimation based on chloroplast sequence variation indicated that the Continental and Mediterranean clades might have been colonized independently during 0.65 ± 0.06 and 0.96 ± 0.1 million years ago (Mya) respectively. The findings of the study will enhance tall fescue breeding for persistence and productivity.</p></div

Classification of tall fescue germplasms collected from Greece based on four selected morphotype-specific chloroplast primers.

<p>The horizontal scale at bottom shows the Nei and Li/dice coefficients.</p

Median network formation for age estimation of diverged groups of 12 <i>Festuca</i> varieties/accessions.

<p>Red circles are the hypothesized median vectors to build the network with maximum parsimony.</p

Morphotype determination of a tall fescue population grown in Oklahoma field with unknown origin using morphotype-specific NFTCHL45 chloroplast primer.

<p>Morphotype determination of a tall fescue population grown in Oklahoma field with unknown origin using morphotype-specific NFTCHL45 chloroplast primer.</p

Name, type and genomic information of 12 <i>Festuca</i> varieties/accessions used in this study.

<p>Name, type and genomic information of 12 <i>Festuca</i> varieties/accessions used in this study.</p

Polymorphism and similarity among tall fescue morphotypes and related species in 20 kb chloroplast sequences.

<p>Polymorphism and similarity index was calculated between the two plant groups in each row.</p

Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene

Increased seed production has been a common goal during the domestication of cereal crops, and early cultivators of barley (Hordeum vulgare ssp. vulgare) selected a phenotype with a six-rowed spike that stably produced three times the usual grain number. This improved yield established barley as a founder crop for the Near Eastern Neolithic civilization. The barley spike has one central and two lateral spikelets at each rachis node. The wild-type progenitor (H. vulgare ssp. spontaneum) has a two-rowed phenotype, with additional, strictly rudimentary, lateral rows; this natural adaptation is advantageous for seed dispersal after shattering. Until recently, the origin of the six-rowed phenotype remained unknown. In the present study, we isolated vrs1 (six-rowed spike 1), the gene responsible for the six-rowed spike in barley, by means of positional cloning. The wild-type Vrs1 allele (for two-rowed barley) encodes a transcription factor that includes a homeodomain with a closely linked leucine zipper motif. Expression of Vrs1 was strictly localized in the lateral-spikelet primordia of immature spikes, suggesting that the VRS1 protein suppresses development of the lateral rows. Loss of function of Vrs1 resulted in complete conversion of the rudimentary lateral spikelets in two-rowed barley into fully developed fertile spikelets in the six-rowed phenotype. Phylogenetic analysis demonstrated that the six-rowed phenotype originated repeatedly, at different times and in different regions, through independent mutations of Vrs1

BAC Libraries from Wheat Chromosome 7D: Efficient Tool for Positional Cloning of Aphid Resistance Genes

Positional cloning in bread wheat is a tedious task due to its huge genome size and hexaploid character. BAC libraries represent an essential tool for positional cloning. However, wheat BAC libraries comprise more than million clones, which makes their screening very laborious. Here, we present a targeted approach based on chromosome-specific BAC libraries. Such libraries were constructed from flow-sorted arms of wheat chromosome 7D. A library from the short arm (7DS) consisting of 49,152 clones with 113 kb insert size represented 12.1 arm equivalents whereas a library from the long arm (7DL) comprised 50,304 clones of 116 kb providing 14.9x arm coverage. The 7DS library was PCR screened with markers linked to Russian wheat aphid resistance gene DnCI2401, the 7DL library was screened by hybridization with a probe linked to greenbug resistance gene Gb3. The small number of clones combined with high coverage made the screening highly efficient and cost effective